U.S. Department of Energy

Pacific Northwest National Laboratory

Insights into immobilizing uranium using nature’s bacterium

A schematic of the custom biofilm reactor.

The Science                      

Due to its respiratory versatilityShewanella oneidensisMR-1 has been widely investigated as a model organism for heavy metal and radionuclide bioremediation. In this studyPNNL researchers developed a mathematical model of S. oneidensisMR-1 biofilms that could help estimate the relative contributions of different biofilm components to total uranium immobilization. Until now, developing such a model was hindered by limitations in the experimental techniques required to investigate biofilms and collect pertinent data.

The Impact

Uranium is an important contaminant because of its prevalence in the environment and its toxicity to many organisms, including humans. In order to reduce environmental exposure to such contaminants, we must understand which organisms to use—and how to use them—for bioremediation. The new mathematical model allows us to predict immobilization of uranium by S. oneidensis MR-1, which helps researchers improve bioremediation techniques and applications.


Microorganisms interact with minerals available in the environment. This has led to the field of bioremediation, in which we use organisms to reduce environmental pollutants. S. oneidensisMR-1 is one type of metal-reducing bacterium that plays an important role in the biogeochemical cycling of many different types of metals and radionuclides. And because the presence of metals and radionuclides can impact cellular metabolism, PNNL researchers believed it was critical to investigate and understand these changes in order to improve bioremediation techniques and applications. 

In this study, researchers considered biofilms, a predominant mode of life for microorganisms. These surface microbial communities (think neighborhoods) are embedded in a matrix of self-produced extracellular polymeric substances, or EPS. Put simply, biofilms consist of cells, bound EPS (those EPS attached to the cell surface), and loosely bound EPS (those EPS that are distributed throughout the biofilm, often in a more soluble form). EPS, in general, comprise 50 to 80 percent of  the organic content of a biofilm; the  rest is comprised of cells. In order to see each of the parts’ contributions in immobilizing uranium, PNNL researchers directed by lead author Ryan Renslow developed a custom nuclear magnetic resonance (NMR) micro-imaging biofilm reactor that allowed them to observe the biofilms in situ.

Their findings indicate that bound EPS and loosely bound EPS immobilize uranium through reduction and adsorption. That is, EPS either binds to the uranium, making it adhere to the biofilm and therefore unable to move, or the EPS chemically changes the uranium so it becomes insoluble. The cells in biofilms, however, appear to be the best uranium immobilizers of all. Immobilization limits exposure by keeping contaminants from moving to wells or rivers.

The study also revealed that the uranium did not significantly affect cell growth or metabolism in the protective biofilms. This is important because bioremediation is dependent upon metabolic activity and cell growth. Previous studies, in fact, have shown that heavy metals and radionuclides inhibit microbial metabolic activity and cell growth, meaning contaminants can negatively alter or slow the metabolism and cell growth of particular organisms. The fact that uranium does not greatly affect the biofilm mode of S. oneidensisMR-1 tells us that the bacterium may be a great candidate for helping improve bioremediation techniques and applications.

Armed with data from the custom bioreactor, researchers used a mathematical model to predict how the biofilms would behave in the presence or absence of uranium. Until now, these predictions had not been possible because of limitations of experimental techniques. The model will need further improvements in order to be able to include multi-species biofilms growing in the subsurface for practical applications. And the model needs to be extended to multiple scales in order to determine the effect of uranium immobilization on the ecosystem. But, until then the model is sufficiently robust and flexible. It can be  modified to include the multiple species or metabolisms that may exist in  bioremediation or in natural scenarios such as those at the U.S. Department of Energy’s  Rifle and Hanford Sites, respectively.


The research was supported by BER, under the SBR Program, and a NIEHS/NIH grant. A portion of the research was performed in EMSL, a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at PNNL. The COMSOL® calculations were performed using the Chinook supercomputer, part of Molecular Science Computing at EMSL. 


Renslow, R., et al.“Modeling Substrate Utilization, Metabolite Production, and Uranium Immobilization in Shewanella oneidensis Biofilms.” Front. Environ. Sci., 29 June 2017 | https://doi.org/10.3389/fenvs.2017.00030.

June 2017
| Pacific Northwest National Laboratory